Strain Fitness in Herbaspirillum seropedicae SmR1 around HSERO_RS23890

Experiment: Plant assay with Setaria viridis; 10 days of inoculation with plant; outgrowth in LB

Add experiment(s):

Zoom: Pan:

Only strains with sufficient reads to estimate fitness are shown, but the strain fitness values are still rather noisy and may be biased towards zero. Strains near the edge of a gene are not shown as being associated with that gene (they are in grey). Strains in the central 10-90% of a gene are color coded by the insertion's strand. Usually, "+" means that the selectable marker is encoded on the forward strand, i.e., transcribed rightward.

download SVG
500 ntHSERO_RS23885 and HSERO_RS23890 are separated by 88 nucleotidesHSERO_RS23890 and HSERO_RS23895 are separated by 271 nucleotidesHSERO_RS23895 and HSERO_RS23900 are separated by 4 nucleotides HSERO_RS23885: HSERO_RS23885 - XRE family transcriptional regulator, at 5,474,833 to 5,475,753 _RS23885 HSERO_RS23890: HSERO_RS23890 - hypothetical protein, at 5,475,842 to 5,476,123 _RS23890 HSERO_RS23895: HSERO_RS23895 - amidophosphoribosyltransferase, at 5,476,395 to 5,476,973 _RS23895 HSERO_RS23900: HSERO_RS23900 - hypothetical protein, at 5,476,978 to 5,477,580 _RS23900 Position (kb) 5475 5476 5477Strain fitness (log2 ratio) -1 0 1 2at 5474.934 kb on - strand, within HSERO_RS23885at 5475.089 kb on + strand, within HSERO_RS23885at 5475.159 kb on - strand, within HSERO_RS23885at 5475.169 kb on - strand, within HSERO_RS23885at 5475.268 kb on + strand, within HSERO_RS23885at 5475.315 kb on + strand, within HSERO_RS23885at 5475.464 kb on + strand, within HSERO_RS23885at 5475.530 kb on - strand, within HSERO_RS23885at 5475.537 kb on + strand, within HSERO_RS23885at 5475.545 kb on - strand, within HSERO_RS23885at 5476.287 kb on + strandat 5476.337 kb on + strandat 5476.461 kb on + strand, within HSERO_RS23895at 5476.471 kb on + strand, within HSERO_RS23895at 5476.499 kb on + strand, within HSERO_RS23895at 5476.594 kb on - strand, within HSERO_RS23895at 5476.700 kb on - strand, within HSERO_RS23895at 5476.745 kb on + strand, within HSERO_RS23895at 5477.105 kb on + strand, within HSERO_RS23900

download strain data

Per-strain Table

Position Strand Gene LocusTag Fraction Plant assay with Setaria viridis; 10 days of inoculation with plant; outgrowth in LB
remove
5,474,934 - HSERO_RS23885 0.11 -0.1
5,475,089 + HSERO_RS23885 0.28 -0.4
5,475,159 - HSERO_RS23885 0.35 +0.9
5,475,169 - HSERO_RS23885 0.36 +2.2
5,475,268 + HSERO_RS23885 0.47 +1.8
5,475,315 + HSERO_RS23885 0.52 +1.6
5,475,464 + HSERO_RS23885 0.69 +1.5
5,475,530 - HSERO_RS23885 0.76 +1.0
5,475,537 + HSERO_RS23885 0.76 +1.7
5,475,545 - HSERO_RS23885 0.77 +2.4
5,476,287 + +0.7
5,476,337 + -0.2
5,476,461 + HSERO_RS23895 0.11 +0.2
5,476,471 + HSERO_RS23895 0.13 +0.2
5,476,499 + HSERO_RS23895 0.18 -0.1
5,476,594 - HSERO_RS23895 0.34 +0.3
5,476,700 - HSERO_RS23895 0.53 +1.0
5,476,745 + HSERO_RS23895 0.60 +0.0
5,477,105 + HSERO_RS23900 0.21 -0.5

Or see this region's nucleotide sequence